A great plot twist could be that the Forerunner technology in Halo is somehow related to an ancient GI Joe artifact. As the two groups explore this connection, they find out that there are hidden powers within these artifacts that could change the fate of both universes. This leads to a race against time as both the Covenant and Cobra also try to get their hands on this power.
Maybe a character from Halo, like Master Chief, gets transported into the GI Joe universe. He has to adapt to their different warfare style and politics. Meanwhile, the GI Joe characters are in awe of his advanced armor and combat abilities. This creates a lot of interesting interactions as they try to figure out how to send him back while also using his skills to fight their own enemies.
One exciting plot twist could be the discovery of a hidden connection between Smallville's Clark Kent and The Flash's Barry Allen that predates their superhero identities. Maybe they are related in some way through their alien or metahuman genetics. Another could be a villain who has the ability to manipulate time and space, causing chaos in both Smallville and Central City. This would force Clark and Barry to work together in ways they haven't before. A third plot twist might be that a character from Smallville who was thought to be normal actually has latent superpowers that are activated during the crossover, adding an unexpected element to the story.
The Spartans' superhuman strength and advanced armor could be combined with GI Joe's stealth and infiltration skills. For example, a Spartan could provide cover fire while a GI Joe operative sneaks in to disable an enemy base's defenses.
One exciting plot twist could be Ben using his alien forms in unexpected ways within the Attack on Titan world. For example, using Heatblast to melt through the Titans' hard exteriors in a crucial battle. Another could be a character from Attack on Titan getting the Omnitrix and having to learn how to use it. This would completely change the power dynamics in the story.
Well, perhaps there could be a crossover where a villain from The Flash, say Reverse - Flash, teams up with a Hydra agent from Agents of Shield. This alliance would be a huge shock as they combine their powers and knowledge. Reverse - Flash's speed and ability to manipulate time along with Hydra's devious plans could create a very difficult situation for the heroes from both universes to handle.
One exciting plot twist could be Spider - Man's web - slinging abilities affecting the Grimm in RWBY. Maybe his webs are able to hold the Grimm in a way that the Huntsmen and Huntresses in RWBY have never seen before. This could change the way battles are fought. Another could be that Spider - Man has to adapt to the world of Remnant, where the rules of physics and combat are different from his own world. For example, he has to figure out how to deal with Dust, the energy source in RWBY, and incorporate it into his fighting style.
Perhaps a major plot twist could be that the tailed beasts in Naruto are somehow connected to the Mother Boxes in the Justice League world. When the Mother Boxes start acting up, it's because the tailed beasts are influencing them. This would force the Justice League and Naruto's friends to work together to figure out how to stop the chaos. Another plot twist could be that the Justice League members are transported to the Naruto world and have to adapt to the ninja way of life, and in the process, they discover new powers within themselves. And finally, if Naruto was able to summon a Justice League member as a summon, like if he could summon Superman instead of a toad, that would be a wild and unexpected plot twist.
One creative plot twist could be that Viewtiful Joe's VFX powers start to malfunction in the School DxD world. This could lead to all kinds of chaos as he tries to control his powers while dealing with the devils and other supernatural beings in School DxD. Another could be that the characters from School DxD gain some of Joe's powers temporarily and have to learn how to use them in their own battles, which would completely change their fighting styles.
Another possible plot twist is if the Forerunners from Halo are somehow related to the ancient magic in Familiar of Zero. Maybe they left behind some technology or knowledge that is now perceived as magic in the Familiar of Zero world. This would open up a whole new avenue of exploration for the characters, as they try to understand the true nature of their powers and the connection between the two universes.
Maybe in the fanfic, there's a villain who can absorb their powers. So when Supergirl and Flash first encounter this villain, they start losing their powers bit by bit. This forces them to rely on their wits and non - superhuman skills to outsmart the villain and find a way to regain their powers before it's too late.
One exciting plot twist could be that Spider - Man's powers are affected by the Sky High environment. Maybe the high altitude messes with his web - shooting ability. Another could be a character from Sky High getting bitten by a radioactive spider - like creature and becoming a new kind of hero. Or perhaps the villains in both universes team up, forcing Spider - Man and the Sky High heroes to work together in ways they never expected.